Configuring a Genome Server

Use the steps described in Loading a Genome to create an initial .genome file and sequence directory. The sequence directory contains a file for each chromosome/contig sequence in the genome.

Copy the sequence directory to a web-accessible directory.

Copy the .genome file (which is a zip archive) to a temporary directory and unzip it.

Remove the .genome file from the temporary directory.

Open the property.txt file in a text editor and edit the following properties:

id: Unique identifier for the genome (for example, "hg18"). This property is input to some commands in igvtools.

name: This is the name that appears in the pull-down genome list in IGV.

sequenceLocation: http:// <path to sequence directory> (this is the location of the sequence directory discussed in step 1 & 2)

Zip all the files in the temporary directory, including the edited property.txt file, and name the resulting archive <id>.genome. This naming convention is mandatory for igvtools.

Copy the <id>.genome file to a web-accessible directory.

To make your genome appear in the users' pull-down list, create a genomes list file. The IGV default genomes list file can be used as a starting point. Each line in the genomes list is formatted as follows:

To test in IGV, change the genome URL in the Advanced preferences tab (View>Preferences) to: http://<path to your genomes.txt file>. You must quit IGV and restart for this preference to take effect. The genome should appear in the drop-down list.